A note on the field of decision analysis

This note provides a short overview of some history, context and concepts in the field of decision analysis. In particular, we describe the connection between normative, prescriptive and descriptive decision theory, and the connection between several different approaches to value and utility

Can insertion length for a double-lumen endobronchial tube be predicted?

Publisher's copy made available with the permission of the publisherIt has been suggested that the appropriate length of insertion for double-lumen tubes can be estimated by external measurement. This study examined the accuracy of external measurement in estimating the actual length of insertion required in 130 patients. It also examined the relationship between the length inserted and the patient’s height in 126 patients and their weight in 125 patients. Although there was a fair correlation between the measured external length and the final inserted length (r=0.61), the 95% confidence intervals of slope and intercept allowed a large variation and the prediction was too wide to be clinically useful. Height was reasonably well correlated with the final length (r=0.51) but an equally wide 95% confidence interval rendered it of little clinical value. There was no correlation between weight and final tube length. It is concluded that external measurement alone is not adequate to predict a clinically acceptable position of the double-lumen tube.R.A. Dyer, S.A.M. Heijke, W.J. Russell, M.B. Bloch, M.F.M. Jameshttp://www.aaic.net.au/Article.asp?D=200004

Comparison of Pollination Graphs

From the agent-based, correlated random walk model presented, we observe the effects of varying the maximum turning angle, δmax, tree density, ω, and pollen carryover, κmax, on the distribution of pollen within a tree population by examining pollination graphs. Varying maximum turning angle and pollen carryover alters the dispersal of pollen, which affects many measures of connectivity of the pollination graph. Among these measures the clustering coefficient of fathers is largest when δmax is between 60 and 90∘. The greatest effect of varying ω is not on the clustering coefficient of fathers, but on the other measures of genetic diversity. In particular when comparing simulations with randomly placed trees with that of actual tree placement of C. florida at the VCU Rice Center, it is clear that having specific tree locations is crucial in determining the properties of a pollination graph

Genomic and bioinformatics analysis of human adenovirus type 37: New insights into corneal tropism

<p>Abstract</p> <p>Background</p> <p>Human adenovirus type 37 (HAdV-37) is a major etiologic agent of epidemic keratoconjunctivitis, a common and severe eye infection associated with long-term visual morbidity due to persistent corneal inflammation. While HAdV-37 has been known for over 20 years as an important cause, the complete genome sequence of this serotype has yet to be reported. A detailed bioinformatics analysis of the genome sequence of HAdV-37 is extremely important to understanding its unique pathogenicity in the eye.</p> <p>Results</p> <p>We sequenced and annotated the complete genome of HAdV-37, and performed genomic and bioinformatics comparisons with other HAdVs to identify differences that might underlie the unique corneal tropism of HAdV-37. Global pairwise genome alignment with HAdV-9, a human species D adenovirus not associated with corneal infection, revealed areas of non-conserved sequence principally in genes for the virus fiber (site of host cell binding), penton (host cell internalization signal), hexon (principal viral capsid structural protein), and E3 (site of several genes that mediate evasion of the host immune system). Phylogenetic analysis revealed close similarities between predicted proteins from HAdV-37 of species D and HAdVs from species B and E. However, virtual 2D gel analyses of predicted viral proteins uncovered unexpected differences in pI and/or size of specific proteins thought to be highly similar by phylogenetics.</p> <p>Conclusion</p> <p>This genomic and bioinformatics analysis of the HAdV-37 genome provides a valuable tool for understanding the corneal tropism of this clinically important virus. Although disparities between HAdV-37 and other HAdV within species D in genes encoding structural and host receptor-binding proteins were to some extent expected, differences in the E3 region suggest as yet unknown roles for this area of the genome. The whole genome comparisons and virtual 2D gel analyses reported herein suggest potent areas for future studies.</p

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B(4)C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources

Prevention and treatment of cardiovascular instability during spinal anaesthesia for caesarean section

Spinal anaesthesia is the method of choice for caesarean section. There is however a significant associated morbidity and mortality in South Africa, particularly in inexperienced hands. This review provides recommendations for safe practice for anaesthetists at all levels of expertise, with particular reference to the management of haemodynamic instability. S Afr Med J 2004; 94: 367-372

Slideflow: Deep Learning for Digital Histopathology with Real-Time Whole-Slide Visualization

Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source options exist for deploying models in an interactive interface. Experimenting with different deep learning approaches typically requires switching software libraries and reprocessing data, reducing the feasibility and practicality of experimenting with new architectures. We developed a flexible deep learning library for histopathology called Slideflow, a package which supports a broad array of deep learning methods for digital pathology and includes a fast whole-slide interface for deploying trained models. Slideflow includes unique tools for whole-slide image data processing, efficient stain normalization and augmentation, weakly-supervised whole-slide classification, uncertainty quantification, feature generation, feature space analysis, and explainability. Whole-slide image processing is highly optimized, enabling whole-slide tile extraction at 40X magnification in 2.5 seconds per slide. The framework-agnostic data processing pipeline enables rapid experimentation with new methods built with either Tensorflow or PyTorch, and the graphical user interface supports real-time visualization of slides, predictions, heatmaps, and feature space characteristics on a variety of hardware devices, including ARM-based devices such as the Raspberry Pi

The Radio Continuum of the Metal-Deficient Blue Compact Dwarf Galaxy SBS0335-052

We present new Very Large Array observations at five frequencies, from 1.4 to 22GHz, of the extremely low-metallicity blue compact dwarf SBS0335-052. The radio spectrum shows considerable absorption at 1.49GHz, and a composite thermal+non-thermal slope. After fitting the data with a variety of models, we find the best-fitting geometry to be one with free-free absorption homogeneously intermixed with the emission of both thermal and non-thermal components. The best-fitting model gives an an emission measure EM ~ 8x10^7pc cm^{-6} and a diameter of the radio-emitting region D ~17pc. The inferred density is n_e ~ 2000 cm^{-3}. The thermal emission comes from an ensemble of \~9000 O7 stars, with a massive star-formation rate (>=5Msun) of 0.13-0.15 yr^{-1}, and a supernova rate of 0.006 yr^{-1}. We find evidence for ionized gas emission from stellar winds, since the observed Bralpha line flux significantly exceeds that inferred from the thermal radio emission. The non-thermal fraction at 5GHz is ~0.7, corresponding to a non-thermal luminosity of ~2x10^{20} W Hz^{-1}. We attribute the non-thermal radio emission to an ensemble of compact SN remnants expanding in a dense interstellar medium, and derive an equipartition magnetic field of ~0.6-1 mG, and a pressure of \~3x10^{-8}-1x10^{-7} dyne cm^{-2}. If the radio properties of SBS0335-052 are representative of star formation in extremely low-metallicity environments, derivations of the star formation rate from the radio continuum in high redshift primordial galaxies need to be reconsidered. Moreover, photometric redshifts inferred from ``standard'' spectral energy distributions could be incorrect.Comment: 25 pages, including 3 figures, accepted for publication in Ap

Peak radial growth of diffuse-porous species occurs during periods of lower water availability than for ring-porous and coniferous trees

Climate models project warmer summer temperatures will increase the frequency and heat severity of droughts in temperate forests of Eastern North America. Hotter droughts are increasingly documented to affect tree growth and forest dynamics, with critical impacts on tree mortality, carbon sequestration and timber provision. The growing acknowledgement of the dominant role of drought timing on tree vulnerability to water deficit raises the issue of our limited understanding of radial growth phenology for most temperate tree species. Here, we use well-replicated dendrometer band data sampled frequently during the growing season to assess the growth phenology of 610 trees from 15 temperate species over 6 years. Patterns of diameter growth follow a typical logistic shape, with growth rates reaching a maximum in June, and then decreasing until process termination. On average, we find that diffuse-porous species take 16-18 days less than other wood-structure types to put on 50% of their annual diameter growth. However, their peak growth rate occurs almost a full month later than ring-porous and conifer species (ca. 24 +/- 4 days; mean +/- 95% credible interval). Unlike other species, the growth phenology of diffuse-porous species in our dataset is highly correlated with their spring foliar phenology. We also find that the later window of growth in diffuse-porous species, coinciding with peak evapotranspiration and lower water availability, exposes them to a higher water deficit of 88 +/- 19 mm (mean +/- SE) during their peak growth than ring-porous and coniferous species (15 +/- 35 mm and 30 +/- 30 mm, respectively). Given the high climatic sensitivity of wood formation, our findings highlight the importance of wood porosity as one predictor of species climatic sensitivity to the projected intensification of the drought regime in the coming decades.Peer reviewe

A New Mass Spectrometer for Upper Atmospheric Measurements in the Auroral Region

We have previously presented a new rocket-borne time-of-flight mass spectrometer (TOF-MS) for measurements in the mesosphere / lower thermosphere (MLT). Traditionally, mass spectrometry in the MLT has been difficult, mainly due to the elevated ambient pressures of the MLT and high speeds of a sounding rocket flight, which affect the direct sampling of the ambient atmosphere and spatial resolution. The TOF-MS is a versatile, inherently adaptable, axial-sampling instrument, capable of operating in a traditional TOF mode or in a multiplexing Hadamard-transform mode where high spatial resolution is desired. To minimize bow shock effects at low altitudes (~70-110km), the ram surface of the TOF-MS can be cryogenically cooled using liquid He to adsorb impinging gas particles. The vacuum pumping system for the TOF-MS is tailored to the specific mission and instrument configuration. Depending on the instrument gas load and operating altitude, cryo, miniature turbo pump or getter-based pumping systems may be employed. Terrestrial TOF-MS instruments often employ a reflectron, essentially an ion-mirror, to improve mass resolving power and compensate for the thermal velocity distribution of particles being measured. The TOF-MS can be arranged in either a simple linear or reflectron configuration. Simulations and modeling are used to compare instrument mass resolution for linear and reflectron configurations for several variable conditions including vehicle velocity and ambient temperature, ultimately demonstrating the potential to make rocket-borne mass spectrometry measurements with unit-mass resolution up to at least 48 amu. Preliminary analyses suggest that many species of interest (including He, CO2, O2, O2 , N2, N2 , and NO ) can be measured with an uncertainty below 10% relative standard deviation on a sounding rocket flight. We also present experimental data for a laboratory prototype linear TOF-MS. Experimental data is compared to simulation and modeling efforts to validate and confirm instrument performance and capability. Two proposed rocket campaigns for investigations of the auroral region include the TOF-MS. By making accurate composition measurements of the neutral atmosphere from 70 to 120km, Mass Spectrometry of the Turbopause Region (MSTR) aims to improve the accuracy of temperature measurements in the turbopause region, improve the MSIS model atmosphere and examine the transition from the turbulently mixed lower atmosphere to the diffusive equilibrium of the upper atmosphere. The ROCKet-borne STorm Energetics of Auroral Dosing in the E-region (ROCK-STEADE) mission will study energy transfer in the E-region during an aurora by examining auroral emissions and measuring concentrations of neutrals and ions. The instrument suite for ROCK-STEADE includes two mass spectrometers, one each to measure neutrals and ions in the altitude range of 70 - 170km. The ability of the TOF-MS instrument to make accurate measurements will greatly aid in better understanding the MLT